VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jan 09 2006 - 16:38:24 CST

Hi,
  I've just been working on updating the APBS plugin in VMD 1.8.4 so
it works with the new APBS 0.4 version which now also runs on Windows,
and things appear to be coming together. If you're interested in trying
a test version of this new APBS plugin, let me know and I'll probably have
a new Windows build of VMD 1.8.4 ready in the near future which includes
the updated APBS plugin.

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Dec 23, 2005 at 09:15:03AM -0800, lily jin wrote:
> I use VMD1.8.4, which is the new version of APBS?
> Thank you and have a great holiday!
>
> John Stone <johns_at_ks.uiuc.edu> wrote:
> Hi,
> There's a new version of APBS that was just released, which apparently
> runs on Windows, but I haven't tried it yet, and I know that the config file
> format has changed, so this may require a new version of VMD and the APBS
> plugin for VMD in order to really use it. I'll write more on this when
> I've had a chance to try it myself.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Dec 21, 2005 at 12:32:36PM -0600, Michel Espinoza-Fonseca wrote:
> > Are you running APBS under windows? Unless you have compiled it for windows, I don't think it will work.
> >
> > ________________________________
> >
> > From: owner-vmd-l_at_ks.uiuc.edu on behalf of lily jin
> > Sent: Wed 12/21/2005 12:14 PM
> > To: vmd-l_at_ks.uiuc.edu
> > Subject: vmd-l: how to use APBS
> >
> >
> > I opened a pdb file 1h8e.pdb with VMD. Then I used Extensions/Analysis/APBS electrostatics
> > I set the path for the files and gave all the parameters in the ELEC values window
> > Then I run APBS.
> > It gave me the following information:
> >
> > info> opened coordinate file C:/PWORK?1h8e.pqr for writing.
> > apbsrun: error runing C:/Program Files/University of Illinois/VMD/plugins/noarch/tcl/apbsrun1.1/apbsrun.tcl
> > apbsrun: error accured while runing APBS:
> > Can't read "apbs_fd": no such variable
> > info> Finished with coordinate file C:/PWORK/1h8e.pqr
> >
> > Can anyone tell me what is the problem? C:/PWORK is the directory I set for the files. I could see the .pqr file was generated in this folder.
> > Thank you very much!
> >
> >
> >
> >
> > Lily
> >
> > __________________________________________________
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> >
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>
>
>
>
> Lily
>
> ---------------------------------
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-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078